Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV–AAVR recognition is in immediate demand. Taking advantage of a particle-filtering algorithm, we report here the cryo-electron microscopy structure of the AAV2–AAVR complex at 2.8 Å resolution. This structure reveals that of the five Ig-like polycystic kidney disease (PKD) domains in AAVR, PKD2 binds directly to the spike region of the AAV2 capsid adjacent to the icosahedral three-fold axis. Residues in strands B and E, and the BC loop of AAVR PKD2 interact directly with the AAV2 capsid. The interacting residues in the AAV2 capsid are mainly in AAV-featured variable regions. Mutagenesis of the amino acids at the AAV2–AAVR interface reduces binding activity and viral infectivity. Our findings provide insights into the biology of AAV entry with high-resolution details, providing opportunities for the development of new AAV vectors for gene therapy.

腺相关病毒 (AAV) 是基于病毒的基因治疗的主要载体。AAV 受体（AAVR；也称为 KIAA0319L）最近被发现，并且迫切需要 AAV-AAVR 识别的精确表征。利用粒子过滤算法，我们在此报告了 AAV2-AAVR 复合物的低温电子显微镜结构，分辨率为 2.8 Å。这种结构揭示了 AAVR 中的五个 Ig 样多囊肾病 (PKD) 结构域中，PKD2 直接结合到与二十面体三重轴相邻的 AAV2 衣壳的尖峰区域。链 B 和 E 中的残基以及 AAVR PKD2 的 BC 环直接与 AAV2 衣壳相互作用。AAV2 衣壳中的相互作用残基主要位于具有 AAV 特征的可变区。AAV2-AAVR 界面处氨基酸的诱变降低了结合活性和病毒感染性。我们的研究结果以高分辨率细节提供了对 AAV 进入生物学的见解，为开发用于基因治疗的新 AAV 载体提供了机会。